A third family of allelic hsd genes in Salmonella enterica: Sequence comparisons with related proteins identify conserved regions implicated in restriction of DNA

Molecular Microbiology

Volumn 22, Issue 3, 1996, Pages 437-447

  Titheradge, Annette J B ^a   Ternent, Diane ^a   Murray, Noreen E ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; DNA MODIFICATION; DNA RESTRICTION; DNA SEQUENCE; NONHUMAN; PRIORITY JOURNAL; SALMONELLA ENTERICA;

ESCHERICHIA; ESCHERICHIA COLI K12; HAEMOPHILUS; HAEMOPHILUS INFLUENZAE RD KW20; SALMONELLA ENTERICA; SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM; TYPHIMURIUM;

EID: 0029845665     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2958.1996.00126.x     Document Type: Article

References (56)

1. Arber, W., and Linn, S. (1969) DNA modification and restriction. Annu Rev Biochem 38: 467-500.
2. Arber, W., and Wauters-Willems, D. (1970) Host specificity of DNA produced by Escherichia coli XII. The two restriction and modification systems of strain 15T . Mol Gen Genet 108: 203-217.
3. Barcus, V.A., and Murray, N.E. (1995) Barriers to recombination: restriction. In Population Genetics of Bacteria. Baumberg, S., Young, J.P.W., Saunders, S.R., and Wellington, E.M.H. (eds). Cambridge, UK: Cambridge University Press, pp. 31-58.
4. Barcus, V.A., Titheradge, A.J.B., and Murray, N.E. (1995) The diversity of alleles at the hsd locus in natural populations of Escherichia coli. Genetics 140: 1187-1197.
5. Bickle, T.A., and Krüger, D.H. (1993) Biology of DNA restriction. Microbiol Rev 57: 434-450.
6. Borck, K., Beggs, J.D., Brammar, W.J., Hopkins, A.S., and Murray, N.B. (1976) The construction in vitro of transducing derivatives of phage lambda. Mol Gen Genet 146: 199-207.
7. Borodovsky, M., and Mclninch, J.D. (1993) GeneMark: parallel gene recognition for both DNA strands. Comput Chen 17 (2): 123-133.
8. Borodovsky, M., Rudd, K.E., and Koonin, E.V. (1994) Intrinsic and extrinsic approaches for detecting genes in a bacterial genome. Nucl Acids Res 22: 4756-4767.
9. Boyer, H.W. (1964) Genetic control of restriction and modification. J Bacteriol 88: 1652-1660.
10. Boyer, H.W., and Roullard-Dussoix, D. (1969) A complementation analysis of the restriction and modification of DNA in Escherichia coli. J Mol Biol 41: 459-472.
11. Bullas, L.R., and Colson, C. (1975) DNA restriction and modification systems in Salmonella. III. SP, a Salmonella potsdam system allelic to the SB system in Salmonella typhimurium. Mol Gen Genet 139: 177-188.
12. Bullas, L.R., Colson, C., and Neufeld, B. (1980) Deoxyribonucleic acid restriction and modification systems in Salmonella: chromosomally located systems of different serotypes. J Bacteriol 141: 275-292.
13. Burland, V., Plunkett, III, G., Sofia, H.J., Daniels, D.L., and Blattner, F.R. (1995) Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 min. Nucl Acids Res 23: 2105-2119.
14. Cowan, G.M., Gann, A.A.F., and Murray, N.E. (1989) Conservation of complex DNA recognition domains between families of restriction enzymes. Cell 56: 103-109.
15. Daniel, A.S., Fuller-Pace, F.V., Legge, D.M., and Murray, N.E. (1988) Distribution and diversity of hsd genes in Escherichia coli and other enteric bacteria. J Bacteriol 170: 1775-1782.
16. Devereux, J., Haeberli, P., and Smithies, O. (1984) A comprehensive set of sequence analysis programs for the VAX. Nucl Acids Res 12: 387-395.
17. Dila, D., Sutherland, E., Moran, L., Slatko, B., and Raleigh, E.A. (1990) Genetic and sequence organisation of the mcrBC locus of Escherichia coli K-1. Bacteriology 172: 4888-4900.
18. Dybvig, K., and Yu, H. (1994) Regulation of a restriction and modification system via DNA inversion in Mycoplasma pulmonis. Mol Microbiol 12: 547-560.
19. Figueroa, F., Günther, E., and Klein, J. (1988) MHC polymorphisms predating speciation. Nature 335: 265-267.
20. Firman, K., Price, C., and Glover, S.W. (1985) The EcoR1241 and EcoR124/3 restriction and modification systems: cloning the genes. Plasmid 14: 224-234.
21. Fleischmann, R.D., et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496-512.
22. Fuller-Pace, F.V., and Murray, N.E. (1986) Two DNA recognition domains of the specificity polypeptides of a family of type I restriction enzymes. Proc Natl Acad Sci USA 83: 9368-9372.
23. Fuller-Pace, F.V., Cowan, G.M., and Murray, N.E. (1985) EcoA and EcoE: alternatives to the EcoK family of type I restriction and modification systems of Escherichia coli. J Mol Biol 186: 65-75.
24. Gorbalenya, A.E., and Koonin, E.V. (1991) Endonuclease (R) subunits of type-I and type-III restriction-modification enzymes contain a helicase-like domain. FEBS Lett 291: 277-281.
25. Gough, J.A., and Murray, N.E. (1983) Sequence diversity among related genes for recognition of specific targets in DNA molecules. J Mol Biol 166: 1-19.
26. Ioerger, T.R., Clark, A.G., and Kao, T.-H. (1990) Polymorphisms at the self-incompatibility locus in Solanaceae predates speciation. Proc Natl Acad Sci USA 87: 9732-9735.
27. Kannan, P., Cowan, G.M., Daniel, A.S., Gann, A.F., and Murray, N.E. (1989) Conservation of organization in the specificity polypeptides of two families of type I restriction enzymes. J Mol Biol 209: 335-344.
28. King, G., and Murray, N.E. (1995) Restriction alleviation and modification enhancement by the Rac prophage of Escherichia coli K-12. Mol Microbiol 16: 769-777.
29. Kües, U., and Cassleton, L.A. (1992) Fungal mating type genes - regulators of sexual development. Mycol Res 96: 993-1006.
30. Kurnit, D.M., and Seed, B. (1990) Improved genetic selection for screening bacteriophage libraries by homologous recombination in vivo. Proc Natl Acad Sci USA 87: 3166-3169.
31. Lawlor, D.A., Ward, F.E., Ennis, P.D., Jackson, A.P., and Parham, P. (1988) HLA-A-B polymorphisms predate the divergence of humans and chimpanzees. Nature 335: 265-267.
32. Lloyd, R.G., and Sharples, G.J. (1993) Processing of recombination intermediates by the RecG and RuvAB proteins of Escherichia coli. Nucl Acids Res 21: 1719-1725.
33. Loenen, W.A.M., Daniel, A.S., Braymer, H.D., and Murray, N.E. (1987) Organization and sequence of the hsd genes of Escherichia coli K-12. J Mol Biol 198: 159-170.
34. Medigue, C., Viari, A., Hénaut, A., and Danchin, A. (1993) Colibri: a functional data base for the Escherichia coli genome. Microbiol Rev 57: 623-654.
35. Murray, N.E. (1983) Phage lambda and molecular cloning. In Lambda II. Hendrix, R.W., Roberts, J.W., Stahl, F.W., and Weisberg, R.A. (eds). Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press, pp. 395-432.
36. Murray, N.E., and Murray, K. (1974) Manipulation of restriction targets in phage λ to form receptor chromosomes for DNA fragments. Nature 251: 476-481.
37. Murray, N.E., Brammar, W.J., and Murray, K. (1977) Lambdoid phages that simplify the recovery of in vitro recombinants. Mol Gen Genet 150: 53-61.
38. Murray, N.E., Gough, J.A., Suri, B., and Bickle, T.A. (1982) Structural homologies among type I restriction-modification systems. EMBO J 1: 535-539.
39. Murray, N.E., Daniel, A.S., Cowan, G.M., and Sharp, P.M. (1993) Conservation of motifs within the unusually variable polypeptide sequences of type I restriction and modification enzymes. Mol Microbiol 9: 133-143.
40. Phadnis, S.H., Huang, H.V., and Berg, D.E. (1989) Tn5supF, a 264-base-pair transposon derived from Tn5 for insertion mutagenesis and sequencing DNAs cloned in phage λ. Proc Natl Acad Sci USA 86: 5908-5912.
41. Price, C., Lingner, J., Bickle, T.A., Firman, K., and Glover, S.W. (1989) Basis for changes in DNA recognition by the EcoR124 and EcoR124/3 type I DNA restriction and modification enzymes. J Mol Biol 205: 115-125.
42. Raleigh, E.A. (1992) Organization and function of the mcrBC genes of Escherichia coli K-12. Mol Microbiol 6: 1079-1086.
43. Raleigh, E.A., Trimarchi, R., and Revel, H. (1989) Genetic and physical mapping of the mcrA (rglA) and mcrB (rglB) loci of Escherichia coli K-12. Genetics 122: 279-296.
44. Redfield, R.J., and Campbell, I.A.M. (1987) Structure of cryptic lambda prophages. J Mol Biol 198: 383-404.
45. Reeves, P. (1993) Evolution of Salmonella O antigen variation by interspecific gene transfer on a large scale. Trends Genet 9: 17-22.
46. Ryu, J.-I., Rajadas, P.T., and Bullas, L.R. (1988) Complementation and hybridization evidence for additional families of type I DNA restriction and modification genes in Salmonella serotypes. J Bacteriol 170: 5785-5788.
47. Sain, B., and Murray, N.B. (1980) The hsd (host specificity) genes of E coli K-12. Mol Gen Genet 180: 35-46.
48. Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual. 2nd edn. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.
49. Sanger, F., Nicklem, S., and Coulsen, A.R. (1977) DNA sequencing and chain-terminating inhibitors. Proc Natl Acad Sci USA 74: 5463-5465.
50. Sharp, P.M., Kelleher, J.E., Daniel, A.S., Cowan, G.M., and Murray, N.E. (1992) Roles of selection and recombination in the evolution of type I restriction-modification systems in enterobacteria. Proc Natl Acad Sci USA 89: 9836-9840.
51. Staden, R. (1982) Automation of the computer handling of gel reading data produced by the shotgun method of DNA sequencing. Nucl Acids Res 10: 4731-4751.
52. Tabor, S., and Richardson, C.C. (1987) DNA sequence analysis with a modified T7 DNA polymerase. Proc Natl Acad Sci USA 84: 4767-4771.
53. Valinluck, B., Lee, N.S., and Ryu, J. (1995) A new restriction-modification system, KpnBI, recognized in Klebsiella pneumoniae. Gene 167: 59-62.
54. Webb, J.L., King, G., Ternent, D., Titheradge, A.J.B., and Murray, N.E. (1996) Restriction by EcoKI is enhanced by co-operative interactions between target sequences and is dependent on DEAD box motifs. EMBO J 15: 2003-2009.
55. Whittaker, P.A., Campbell, A.J.B., Southern, E.M., and Murray, N.E. (1988) Enhanced recovery and restriction mapping of DNA fragments cloned in a new λ vector. Nucl Acids Res 16: 6725-6736.
56. Xu, G., Willert, J., Kapfer, W., and Trautner, T. A. (1995) BsuCI, a type-I restriction-modification system in Bacillus subtilis. Gene 157: 59.